Commands Index

The following are commands entered into Chimera's Command Line. Each command (but not its keywords, unless explicitly indicated) may be shortened to a unique prefix. Many commands act upon specified atoms. Past commands can be accessed using the Command History. Multiple commands can be placed in a file.

⁺ significantly changed or enhanced in Chimera relative to MidasPlus
^U UNIX only (not on Windows)
^C Chimera only (not available in MidasPlus)

2dlabels^C - create arbitrary text labels and place them in 2D
ac^C - enable the use of accelerators (keyboard shortcuts)
addaa - add an amino acid to a peptide C-terminus
addh^C - add hydrogens
alias - create an alias or list existing aliases
align - align two atoms along the line of sight
angle - measure a bond angle or torsion angle
bond - add/delete bonds
bondcolor^C - color bonds independently from atoms
bonddisplay^C - control how bond display depends on atom display
bondrepr^C - control the representation of bonds (wire or stick)
brotation - make a bond rotatable
cd - change the working directory
center - center the view on specified atoms
chain - chain specified atoms, undisplay the others
chirality^C - report the R/S configuration of a chiral center
clip - move clipping planes
close - close a model
cofr - report or change the center of rotation
color⁺ - color atoms/bonds, ribbons, labels, and surfaces
colordef - define a new color
conic - create a static space-filling rendering with shadows
copy⁺ - save or print the displayed image
defattr^C - assign attribute values to atoms, residues, or models
delete⁺ - delete atoms and bonds
display - display and undisplay atoms
distance - measure the distance between two atoms
echo - send text to the Reply Log
findhbond^C - identify possible hydrogen bonds
focus^C - adjust the view and center of rotation to the displayed and specified atoms
freeze - stop all motion
getcrd - report untransformed coordinates
hbonds^C - identify possible hydrogen bonds
help - display the manual page for a command
ksdssp - determine secondary structure from protein coordinates
label - display atom labels
labelopt^C - control the information in atom labels
linewidth^C - control the width of lines in the wire representation
load - restore a saved Chimera session
longbond - find and remove excessively long bonds
match - superimpose two models by a least-squares fit of specified atoms
matchmaker^C - align models in sequence and then superimpose them accordingly
matrixcopy - apply the transformation matrix of one model to another
matrixget - write the current transformation matrices to a file
matrixset - read and apply transformation matrices from a file
mmaker^C - align models in sequence and then superimpose them accordingly
modelcolor^C - set color at the model level
modeldisplay^C - set display at the model level
move - translate along the X, Y, or Z axis
movie^C - capture image frames and assemble them into a movie file
msms^C - (see surfcat/surfrepr)
neon^U - create a static space-filling or stick rendering with shadows
objdisplay - display and undisplay VRML models
open⁺ - open structures or data for display or execute a command file
pdbrun - send an annotated PDB file of the current display to the system shell
push/pop - push or pop images on the picture stack
rainbow - color residues, chains, models over a range (default blue to red)
rangecolor^C - color over a range according to attribute values
read - execute a command file, only updating the display at the end
represent^C - control the representation of atoms and bonds (wire, stick, ball-and-stick, or sphere)
reset - restore default or saved orientations
ribbackbone^C - allow ribbon and all backbone atoms to be displayed simultaneously for residues within a model
ribbon^C - display a secondary structure ribbon
ribbonjr^U - create a static ribbon rendering
ribcolor^C - set ribbon color
ribrepr^C - control the ribbon representation (flat, sharp, or smooth)
rlabel⁺ - display residue labels
rmsd^C - evaluate the RMSD between specified sets of atoms
rock - rock back and forth about the X, Y, or Z axis
roll - rotate about the X, Y, or Z axis
rotation - make a bond rotatable
save - save the current Chimera session
savepos - save the current orientations
scale - scale the view
section - move the clipping planes in parallel
select⁺ - activate models for motion or select atoms for further operations
set/unset - set options
show - display specified atoms, undisplay the others
sleep - suspend command processing for a specified length of time
source - execute a command file, updating the view continually
stereo - switch amongst stereo options and mono viewing
stop - exit from Chimera
surface⁺ - calculate and display molecular surface
surfcat/surfrepr^C - create molecular surface categories and control the surface representation
surfcolor^C - set whether surface color is determined at the atom or model level
swapaa - mutate amino acid residues
swapna - mutate nucleic acid residues
system - send a command to the system shell
tcolor^C - color atoms/bonds, labels, and surfaces with a texture color
texture^C - define texture maps and associated colors
thickness - move the clipping planes in opposite directions
turn - rotate about the X, Y, or Z axis
vdw - display van der Waals (VDW) dot surface
vdwdefine^C - set VDW radii
vdwdensity^C - set VDW surface dot density
version - show copyright information and which version of Chimera is being used
wait - suspend command processing a specified number of frames or until motion has stopped
window - adjust the view to contain the displayed and specified atoms
write⁺ - save all or part of a molecule model as a PDB file
writesel^C - write a parsable text file containing specifications of the currently selected (or unselected) items
x3dsave^C - save the graphical scene as an X3D file

Of the Midas commands unsupported by Chimera, some may be implemented in the future; others have been rendered obsolete or replaced by other functionality.

Command Files

Files of commands can be created manually or saved using the Command History. Certain commands are especially useful for scripting continuous motion. Comments are indicated by # at the beginning of a line. Any files opened by a command file must be in the working directory, or their full pathnames supplied.

A command file can be executed:

• with the command read (the display will not update until the last command has executed)
• with the command source (the display will update as each command executes)
• by opening the file, if its type is specified properly (updates the display like source)
• automatically when the Command Line is started (see the Midas preferences; updates the display like source)